Job ID = 11192566 sra ファイルのダウンロード中... Completed: 2202150K bytes transferred in 22 seconds (819260K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 67516288 spots for /home/okishinya/chipatlas/results/rn6/SRX2226580/SRR4374830.sra Written 67516288 spots for /home/okishinya/chipatlas/results/rn6/SRX2226580/SRR4374830.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:44:59 67516288 reads; of these: 67516288 (100.00%) were unpaired; of these: 14480884 (21.45%) aligned 0 times 39867994 (59.05%) aligned exactly 1 time 13167410 (19.50%) aligned >1 times 78.55% overall alignment rate Time searching: 00:45:03 Overall time: 00:45:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 24 files... [bam_rmdupse_core] 43613045 / 53035404 = 0.8223 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 15 Sep 2018 09:53:55: # Command line: callpeak -t SRX2226580.bam -f BAM -g 2.15e9 -n SRX2226580.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226580.05 # format = BAM # ChIP-seq file = ['SRX2226580.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Sep 2018 09:53:55: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:53:55: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:53:55: # Command line: callpeak -t SRX2226580.bam -f BAM -g 2.15e9 -n SRX2226580.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226580.20 # format = BAM # ChIP-seq file = ['SRX2226580.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Sep 2018 09:53:55: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:53:55: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:53:55: # Command line: callpeak -t SRX2226580.bam -f BAM -g 2.15e9 -n SRX2226580.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226580.10 # format = BAM # ChIP-seq file = ['SRX2226580.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Sep 2018 09:53:55: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:53:55: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:54:01: 1000000 INFO @ Sat, 15 Sep 2018 09:54:02: 1000000 INFO @ Sat, 15 Sep 2018 09:54:02: 1000000 INFO @ Sat, 15 Sep 2018 09:54:08: 2000000 INFO @ Sat, 15 Sep 2018 09:54:09: 2000000 INFO @ Sat, 15 Sep 2018 09:54:10: 2000000 INFO @ Sat, 15 Sep 2018 09:54:15: 3000000 INFO @ Sat, 15 Sep 2018 09:54:15: 3000000 INFO @ Sat, 15 Sep 2018 09:54:17: 3000000 INFO @ Sat, 15 Sep 2018 09:54:22: 4000000 INFO @ Sat, 15 Sep 2018 09:54:23: 4000000 INFO @ Sat, 15 Sep 2018 09:54:26: 4000000 INFO @ Sat, 15 Sep 2018 09:54:30: 5000000 INFO @ Sat, 15 Sep 2018 09:54:31: 5000000 INFO @ Sat, 15 Sep 2018 09:54:34: 5000000 INFO @ Sat, 15 Sep 2018 09:54:37: 6000000 INFO @ Sat, 15 Sep 2018 09:54:38: 6000000 INFO @ Sat, 15 Sep 2018 09:54:41: 6000000 INFO @ Sat, 15 Sep 2018 09:54:44: 7000000 INFO @ Sat, 15 Sep 2018 09:54:45: 7000000 INFO @ Sat, 15 Sep 2018 09:54:48: 7000000 INFO @ Sat, 15 Sep 2018 09:54:51: 8000000 INFO @ Sat, 15 Sep 2018 09:54:52: 8000000 INFO @ Sat, 15 Sep 2018 09:54:55: 8000000 INFO @ Sat, 15 Sep 2018 09:54:58: 9000000 INFO @ Sat, 15 Sep 2018 09:55:00: 9000000 INFO @ Sat, 15 Sep 2018 09:55:01: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:55:01: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:55:01: #1 total tags in treatment: 9422359 INFO @ Sat, 15 Sep 2018 09:55:01: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:55:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:55:01: #1 tags after filtering in treatment: 9422188 INFO @ Sat, 15 Sep 2018 09:55:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:55:01: #1 finished! INFO @ Sat, 15 Sep 2018 09:55:01: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:55:03: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:55:03: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:55:03: #1 total tags in treatment: 9422359 INFO @ Sat, 15 Sep 2018 09:55:03: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:55:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:55:03: 9000000 INFO @ Sat, 15 Sep 2018 09:55:03: #1 tags after filtering in treatment: 9422188 INFO @ Sat, 15 Sep 2018 09:55:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:55:03: #1 finished! INFO @ Sat, 15 Sep 2018 09:55:03: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:55:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:55:05: #2 number of paired peaks: 78474 INFO @ Sat, 15 Sep 2018 09:55:05: start model_add_line... INFO @ Sat, 15 Sep 2018 09:55:05: start X-correlation... INFO @ Sat, 15 Sep 2018 09:55:05: end of X-cor INFO @ Sat, 15 Sep 2018 09:55:05: #2 finished! INFO @ Sat, 15 Sep 2018 09:55:05: #2 predicted fragment length is 251 bps INFO @ Sat, 15 Sep 2018 09:55:05: #2 alternative fragment length(s) may be 251 bps INFO @ Sat, 15 Sep 2018 09:55:05: #2.2 Generate R script for model : SRX2226580.05_model.r INFO @ Sat, 15 Sep 2018 09:55:05: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:55:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:55:06: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:55:06: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:55:06: #1 total tags in treatment: 9422359 INFO @ Sat, 15 Sep 2018 09:55:06: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:55:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:55:06: #1 tags after filtering in treatment: 9422188 INFO @ Sat, 15 Sep 2018 09:55:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:55:06: #1 finished! INFO @ Sat, 15 Sep 2018 09:55:06: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:55:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:55:07: #2 number of paired peaks: 78474 INFO @ Sat, 15 Sep 2018 09:55:07: start model_add_line... INFO @ Sat, 15 Sep 2018 09:55:07: start X-correlation... INFO @ Sat, 15 Sep 2018 09:55:07: end of X-cor INFO @ Sat, 15 Sep 2018 09:55:07: #2 finished! INFO @ Sat, 15 Sep 2018 09:55:07: #2 predicted fragment length is 251 bps INFO @ Sat, 15 Sep 2018 09:55:07: #2 alternative fragment length(s) may be 251 bps INFO @ Sat, 15 Sep 2018 09:55:07: #2.2 Generate R script for model : SRX2226580.20_model.r INFO @ Sat, 15 Sep 2018 09:55:07: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:55:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:55:10: #2 number of paired peaks: 78474 INFO @ Sat, 15 Sep 2018 09:55:10: start model_add_line... INFO @ Sat, 15 Sep 2018 09:55:10: start X-correlation... INFO @ Sat, 15 Sep 2018 09:55:10: end of X-cor INFO @ Sat, 15 Sep 2018 09:55:10: #2 finished! INFO @ Sat, 15 Sep 2018 09:55:10: #2 predicted fragment length is 251 bps INFO @ Sat, 15 Sep 2018 09:55:10: #2 alternative fragment length(s) may be 251 bps INFO @ Sat, 15 Sep 2018 09:55:10: #2.2 Generate R script for model : SRX2226580.10_model.r INFO @ Sat, 15 Sep 2018 09:55:10: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:55:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:55:29: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:55:31: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:55:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:55:44: #4 Write output xls file... SRX2226580.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:55:44: #4 Write peak in narrowPeak format file... SRX2226580.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:55:44: #4 Write summits bed file... SRX2226580.05_summits.bed INFO @ Sat, 15 Sep 2018 09:55:44: Done! pass1 - making usageList (117 chroms): 2 millis pass2 - checking and writing primary data (7400 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:55:46: #4 Write output xls file... SRX2226580.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:55:46: #4 Write peak in narrowPeak format file... SRX2226580.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:55:46: #4 Write summits bed file... SRX2226580.20_summits.bed INFO @ Sat, 15 Sep 2018 09:55:46: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:55:49: #4 Write output xls file... SRX2226580.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:55:49: #4 Write peak in narrowPeak format file... SRX2226580.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:55:49: #4 Write summits bed file... SRX2226580.10_summits.bed INFO @ Sat, 15 Sep 2018 09:55:49: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (1669 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。